Fastq quliaty score and MAQ output quality score

[baohua100]

fastq file:
@I326_2_FC306FCAAXX:8:1:50:985
ATGTCCGAAGGGCAGTCTCAAGTGGTAAAATGGAT
+I326_2_FC306FCAAXX:8:1:50:985
hhhWhhhchhhhhahShh\PO]LgXZXPNLUTZNO


MAQ alignment output:

I326_2_FC306FCAAXX:8:1:50:985 1 1 + 0 0 99 99 99 0 0 1 0 35 ATGTCCGAAGGGCAGTCTCAAGTGGTAAAATGGAT ```W```````````S``\PO]L`XZXPNLUTZNO

what's the meaning of ```W```````````S``\PO]L`XZXPNLUTZNO ?

not the same as hhhWhhhchhhhhahShh\PO]LgXZXPNLUTZNO

[swbarnes2]

Well, they actually look pretty similar, the first one is maintaining distinctions between the quality of 7th and 8th letters, for instance, while Maq is treating them the same.

Is it possible that your fastq is flipped in orientation, and those are the low quality letters first? Maybe the first one is splitting out the low quality scores much finer than Maq.